After a rain today I was bringing in the slide on my 2016 Heritage Glen 368rlbh and a bunch of water ran in off the roof of the slide into the camper. I have not had that happen on previous 5th wheel campers. If it matters this is the first unit I have had slide toppers on.
There you go....proof that slide toppers are not going to prevent all rain water from getting on the slide top. Just takes a driving wind and it will get there, as will leaves and other debris.
The 'wiper' gaskets should sweep that water and keep 90%+ of the water outside. I'd imagine you have a gasket that didn't flip properly when you pulled it in. Either that or they're damaged.
Give them a thorough inspection and condition them with the gasket/slide conditioner. I spray it on and wipe off with a rag covering as mush of both sides as possible.
Don't forget there are multiple sets of gaskets. Outside set and inside set.